#!/bin/bash

# Parameters.
prog=/home/jlindsay/code/FeatureCorrelate/src/feature_correlate.py
query=/data2/projects/tammar_analysis/mirbase/blat_mirbase.gff
tbase=/data2/projects/tammar_analysis/maps/tammar_crasi_tammar
odir=/data2/projects/tammar_analysis/mirbase/overlap

targets[0]=tammar12_Wallaby_testis_lower_split00.sam
targets[1]=tammar12_Wallaby_testis_lower_split01.sam
targets[2]=tammar12_Wallaby_testis_lower_split02.sam
targets[3]=tammar12_Wallaby_testis_lower_split03.sam
targets[4]=tammar12_Wallaby_testis_lower_split04.sam
targets[5]=tammar12_Wallaby_testis_lower_split05.sam
targets[6]=tammar12_Wallaby_testis_lower_split06.sam
targets[7]=tammar12_Wallaby_testis_lower_split07.sam
targets[8]=tammar12_Wallaby_testis_lower_split08.sam
targets[9]=tammar12_Wallaby_testis_lower_split09.sam
targets[20]=tammar12_Wallaby_testis_lower_split10.sam
targets[11]=tammar12_Wallaby_testis_lower_split11.sam
targets[12]=tammar12_Wallaby_testis_lower_split12.sam
targets[13]=tammar12_Wallaby_testis_lower_split13.sam
targets[14]=tammar12_Wallaby_testis_lower_split14.sam
targets[15]=tammar12_Wallaby_brain.sam
targets[16]=tammar12_Wallaby_fibroblasts.sam
targets[17]=tammar12_Wallaby_liver.sam
targets[18]=tammar12_Wallaby_ovary_lower.sam

# Loop over targets.
for t in ${targets[@]}; do
	# Match query to targets.
	python $prog -m correlate -r both -s 500 -t $tbase/$t -q $query -o ${odir}/$t
done;
